Professional diver Gregg Bemis of Santa Fe, New Mexico, and German TV producer Jutta Rabe led the expedition to the wreck despite opposition from the Swedish government.
Bemis and Rabe face prison sentences of up to two years if they travel to Sweden.
The expedition was closely supervised by the Swedish coast guard, but could not be stopped because the wreck lies in international waters.
Prosecutor Ronnie Jacobsson said he hadn't decided yet whether to issue an international warrant and he did not believe that the United States or Germany would extradite their own citizens.
Bemis, who said he organized the filmed dive to find further clues to why the ferry sank, dismissed the arrest warrant, saying he did not plan to travel to Sweden anytime soon.
"I think they are going after the wrong target," Bemis told AP in a telephone interview from New Mexico. "I think they should be more concerned with the 852 people who were murdered than two people who tried to do some honest research."
Bemis claimed the ferry sinking was not an accident, but declined further details, saying he would release more information "within a couple of weeks."
Sweden, Finland, Estonia, Denmark, Lithuania, Russia and Great Britain signed an agreement to declare the wreck site a final resting place for the victims and make criminal activities disturbing it. In one of Europe's worst maritime disasters, the Estonia sank in a storm off the Finnish coast en route from Tallinn to Stockholm on Sept. 28, 1994. Only 137 people survived, and rescuers recovered and identified 94 bodies.